If you haven't already I highly recommend you check out the original
ptraj clustering paper by Cheatham et al (J. Chem. Theory Comput.,
2007, 3 (6), pp 2312–2334,
http://pubs.acs.org/doi/abs/10.1021/ct700119m) which has in-depth
analysis and discussion of various clustering algorithms applied to MD
trajectories.
-Dan
On Thu, Feb 2, 2017 at 3:46 AM, Sowmya Indrakumar <soemya.kemi.dtu.dk> wrote:
> Dear Ravi,
> Thank you for this email. It was very informative.
> I now understand, avergelinkage is a heirarchial agglomerative clustering method using RMSD metrics. (bottoms up aprroach) and hence there is no consideration of any reference initial structure.
>
> Thank you once again.
> Regards
> Sowmya
> ________________________________________
> From: Ravi Abrol [raviabrol.gmail.com]
> Sent: Thursday, February 02, 2017 12:08 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] clustering
>
> Hello Sowmya,
>
> You are asking a couple of different questions.
>
> First, how the clustering method partitions the trajectory frames into
> different clusters and how the
> different clusters are ordered during output. This depends on the method
> used and in your case,
> the cpptraj documentation will have that answer.
>
> Second is the use of an "average" structure. If large conformational
> changes are going on, then there
> is no good average structure. If you really need an average structure, the
> "raw" average structure
> obtained by averaging x,y,z over all trajectory frames is almost always
> unphysical as Bill Ross pointed out.
> A "realistic" average structure can be obtained by comparing all the
> trajectory frames to the "raw"
> average structure and picking "the" frame that has the smallest RMSD to the
> "raw" average structure.
>
> Ravi
>
> ---
> On Wed, Feb 1, 2017 at 3:41 AM, Sowmya Indrakumar <soemya.kemi.dtu.dk>
> wrote:
>
>> Dear Daniel and Bill,
>> Thank you for your suggestions.
>> I was expecting RMSD to increase with the cluster number, for instance
>> RMSD of the representative structure to the average structure should be the
>> least considered to the last cluster representative structure to the
>> average). Since here, the frames are partitioned into distinct clusters, we
>> don't take into account any reference structure.
>>
>> But as you suggested, comparing to the average structure doesn't make
>> sense if there is a lot of changes.
>> It is still not clear how frames are put into distinct cluster, does it
>> compare all the frames and then assign them to various clusters?
>>
>> Thanks
>> Regards
>> SOwmya
>>
>> ________________________________________
>> From: Bill Ross [ross.cgl.ucsf.edu]
>> Sent: Tuesday, January 31, 2017 7:11 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] clustering
>>
>> Not sure if it has been pointed out, but average structures from
>> trajectories can be quite unrealistic if the system has interesting
>> changes going on.
>>
>> Bill
>>
>>
>> On 1/31/17 9:59 AM, Daniel Roe wrote:
>> > On Tue, Jan 31, 2017 at 10:03 AM, Sowmya Indrakumar <soemya.kemi.dtu.dk>
>> wrote:
>> >> running the above commands gives me 5 representative structures. It is
>> not very clear to me what is it taking as the reference structure.
>> Comparing the five generated representative pdb structure to the average
>> pdb (from the trajectory) does not give show any trend in RMSD.
>> > The representative structure of each cluster is the frame with the
>> > lowest cumulative "distance" (in your case RMSD) to every other frame
>> > in the cluster. A cluster representative is just that; it's supposed
>> > to be representative of what that cluster looks like (although this
>> > may not always be the case). I can see how comparing representative
>> > structures to the average structure of the cluster could be
>> > informative ('avgout', 'avgfmt'), but it's not clear to me what
>> > insight you can gain from comparing representatives to the overall
>> > average structure.
>> >
>> > -Dan
>> >
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Feb 02 2017 - 07:00:02 PST
